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- PDB-2ddi: NMR structure of the second Kunitz domain of human WFIKKN1 -

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Basic information

Entry
Database: PDB / ID: 2ddi
TitleNMR structure of the second Kunitz domain of human WFIKKN1
ComponentsWAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1
KeywordsPROTEIN BINDING / Kunitz domain
Function / homology
Function and homology information


receptor antagonist activity / muscle cell development / transforming growth factor beta binding / roof of mouth development / transforming growth factor beta receptor signaling pathway / skeletal system development / negative regulation of transforming growth factor beta receptor signaling pathway / serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 1/2 / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Pancreatic trypsin inhibitor Kunitz domain ...WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 1/2 / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Pancreatic trypsin inhibitor Kunitz domain / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Few Secondary Structures / Irregular / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLiepinsh, E. / Otting, G.
CitationJournal: J.Biomol.Nmr / Year: 2006
Title: Second Kunitz-type protease inhibitor domain of the human WFIKKN1 protein
Authors: Liepinsh, E. / Nagy, A. / Trexler, M. / Patthy, L. / Otting, G.
History
DepositionJan 30, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1


Theoretical massNumber of molelcules
Total (without water)7,8791
Polymers7,8791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1 / WFIKKN1 / trypsin inhibitor


Mass: 7878.603 Da / Num. of mol.: 1 / Fragment: second Kunitz domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WFIKKN1 / Plasmid: pPICZalfaA / Cell line (production host): GS115 (his4) / Production host: Pichia pastoris (fungus) / References: GenBank: 75517744, UniProt: Q96NZ8*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
132DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM Kunitz domain; 90% H2O, 10% D2O90% H2O/10% D2O
21.1 mM Kunitz domain; 100% D2O100% D2O
Sample conditionsIonic strength: 10 mM / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
OPAL2.6refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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